faculty – Page 12 – Penn Bioengineering Blog

June 9, 2023

2023 Department of Bioengineering Juneteenth Address: “A White Neighbor, a Black Surgeon, and a Mormon Computer Scientist Walk into a Bar…” (Kevin B. Johnson)

We hope you will join us for the 2023 Department of Bioengineering Juneteenth Address by Dr. Kevin B. Johnson.

Date: Wednesday, June 14, 2023
Start Time: 11:00 AM ET
Location: Berger Auditorium (Skirkanich Hall basement room 013)

Zoom link
Meeting ID: 925 0325 6013
Passcode: 801060

Following the event, a limited number of box lunches will be available for in-person attendees. If you would like a box lunch, please RSVP here by Monday, June 12 so we can get an accurate headcount.

Speaker: Kevin B. Johnson, MD, MS, FAAP, FAMIA, FACMI
David L. Cohen University Professor
Annenberg School for Communication, Bioengineering, Biostatistics, Epidemiology and Informatics, Computer and Information Science, Pediatrics
VP for Applied Informatics (UPHS), University of Pennsylvania

Title: “A White Neighbor, a Black Surgeon, and a Mormon Computer Scientist Walk into a Bar…”

Abstract: As we recognize Juneteenth, a holiday that brings awareness to what journalist Corey Mitchell calls “…a complex understanding of the nation’s past”, we also need to understand how many of our neighbors, staff, and faculty—even those born in the last 100 years—continue to navigate through the environment that made Juneteenth remarkable. Dr. Johnson will share a bit of his personal story and how this story informs his national service and passion for teaching.

Bio: Dr. Johnson is a leader of medical information technologies to improve patient care and safety. He is well regarded and widely known for pioneering discoveries in clinical informatics, leading to advances in data acquisition, medication management, and information aggregation in medical settings.

He is a board-certified pediatrician who has aligned the powers of medicine, engineering and technology to improve the health of individuals and communities. In work that bridges biomedical informatics, bioengineering and computer science, he has championed the development and implementation of clinical information systems and artificial intelligence to drive medical research. He has encouraged the effective use of technology at the bedside, and he has empowered patients to use new tools that help them to understand how medications and supplements may affect their health. He is interested in using advanced technologies such as smart devices and in developing computer-based documentation systems for the point of care. He also is an emerging champion of the use of digital media to enhance science communication, with a successful feature-length documentary describing health information exchange, a podcast (Informatics in the Round) and most recently, a children’s book series aimed at STEM education featuring scientists underrepresented in healthcare.

Dr. Johnson holds joint appointments in the Department of Computer and Information Science of the School of Engineering and Applied Science, and secondary appointments in Bioengineering and the Annenberg School for Communication. He serves as Vice President for Applied Informatics in the University of Pennsylvania Health System and as a Professor of Pediatrics at the Children’s Hospital of Philadelphia.

Before arriving at Penn, he served as the Cornelius Vanderbilt Professor and Chair of the Department of Biomedical Informatics at the Vanderbilt University School of Medicine, where he had taught since 2002. As Senior Vice President for Health Information Technology at the Vanderbilt University Medical Center, he led the development of clinical systems that enabled doctors to make better treatment and care decisions for individual patients, and introduced new systems to integrate artificial intelligence into patient care workflows.

The author of more than 150 publications, Dr. Johnson has held numerous leadership positions in the American Medical Informatics Association and the American Academy of Pediatrics. He leads the American Board of Pediatrics Informatics Advisory Committee, directs the Board of Scientific Counselors of the National Library of Medicine, and is a member of the NIH Council of Councils. He is an elected member of the National Academy of Medicine, American College of Medical Informatics and Academic Pediatric Society. He has received awards from the Robert Wood Johnson Foundation and American Academy of Pediatrics, among many others.

June 7, 2023

Nanorobotic Systems Presents New Options for Targeting Fungal Infections

by Nathi Magubane

Candida albicans is a species of yeast that is a normal part of the human microbiota but can also cause severe infections that pose a significant global health risk due to their resistance to existing treatments, so much so that the World Health Organization has highlighted this as a priority issue. The picture above shows a before (left) and after (right) fluorescence image of fungal biofilms being precisely targeted by nanozyme microrobots without bonding to or disturbing the tissue sample. (Image: Min Jun Oh and Seokyoung Yoon)

Infections caused by fungi, such as Candida albicans, pose a significant global health risk due to their resistance to existing treatments, so much so that the World Health Organization has highlighted this as a priority issue.

Although nanomaterials show promise as antifungal agents, current iterations lack the potency and specificity needed for quick and targeted treatment, leading to prolonged treatment times and potential off-target effects and drug resistance.

Now, in a groundbreaking development with far-reaching implications for global health, a team of researchers jointly led by Hyun (Michel) Koo of the University of Pennsylvania School of Dental Medicine and Edward Steager of Penn’s School of Engineering and Applied Science has created a microrobotic system capable of rapid, targeted elimination of fungal pathogens.

“Candida forms tenacious biofilm infections that are particularly hard to treat,” Koo says. “Current antifungal therapies lack the potency and specificity required to quickly and effectively eliminate these pathogens, so this collaboration draws from our clinical knowledge and combines Ed’s team and their robotic expertise to offer a new approach.”

The team of researchers is a part of Penn Dental’s Center for Innovation & Precision Dentistry, an initiative that leverages engineering and computational approaches to uncover new knowledge for disease mitigation and advance oral and craniofacial health care innovation.

For this paper, published in Advanced Materials, the researchers capitalized on recent advancements in catalytic nanoparticles, known as nanozymes, and they built miniature robotic systems that could accurately target and quickly destroy fungal cells. They achieved this by using electromagnetic fields to control the shape and movements of these nanozyme microrobots with great precision.

“The methods we use to control the nanoparticles in this study are magnetic, which allows us to direct them to the exact infection location,” Steager says. “We use iron oxide nanoparticles, which have another important property, namely that they’re catalytic.”

Read the full story in Penn Today.

Hyun (Michel) Koo is a professor in the Department of Orthodontics and in the divisions of Pediatric Dentistry and Community Oral Health and is the co-founder of the Center for Innovation & Precision Dentistry in the School of Dental Medicine at the University of Pennsylvania. He is a member of the Penn Bioengineering Graduate Group.

Edward Steager is a research investigator in the School of Engineering and Applied Science’s General Robotics, Automation, Sensing & Perception Laboratory at Penn.

Other authors include Min Jun Oh, Alaa Babeer, Yuan Liu, Zhi Ren, Zhenting Xiang, Yilan Miao, and Chider Chen of Penn Dental; and David P. Cormode and Seokyoung Yoon of the Perelman School of Medicine. Cormode also holds a secondary appointment in Bioengineering.

This research was supported in part by the National Institute for Dental and Craniofacial Research (R01 DE025848, R56 DE029985, R90DE031532 and; the Basic Science Research Program through the National Research Foundation of Korea of the Ministry of Education (NRF-2021R1A6A3A03044553).

June 1, 2023May 31, 2023

Folding@Home: How You, and Your Computer, Can Play Scientist

by Alex Gardner

Greg Bowman kneels, working on a server. — Folding@home is led by Gregory Bowman, a Penn Integrates Knowledge Professor who has appointments in the Departments of Biochemistry and Biophysics in the Perelman School of Medicine and the Department of Bioengineering in the School of Engineering and Applied Science. (Image: Courtesy of Penn Medicine News)

Two heads are better than one. The ethos behind the scientific research project Folding@home is that same idea, multiplied: 50,000 computers are better than one.

Folding@home is a distributed computing project which is used to simulate protein folding, or how protein molecules assemble themselves into 3-D shapes. Research into protein folding allows scientists to better understand how these molecules function or malfunction inside the human body. Often, mutations in proteins influence the progression of many diseases like Alzheimer’s disease, cancer, and even COVID-19.

Penn is home to both the computer brains and human minds behind the Folding@home project which, with its network, forms the largest supercomputer in the world. All of that computing power continually works together to answer scientific questions such as what areas of specific protein implicated in Parkinson’s disease may be susceptible to medication or other treatment.

Led by Gregory Bowman, a Penn Integrates Knowledge professor of Biochemistry and Biophysics in the Perelman School of Medicine who has joint appointments in the Department of Biochemistry and Biophysics in the Perelman School of Medicine and the Department of Bioengineering in the School of Engineering and Applied Science, Folding@home is open for any individual around the world to participate in and essentially volunteer their computer to join a huge network of computers and do research.

Using the network hub at Penn, Bowman and his team assign experiments to each individual computer which communicates with other computers and feeds info back to Philly. To date, the network is comprised of more than 50,000 computers spread across the world.

“What we do is like drawing a map,” said Bowman, explaining how the networked computers work together in a type of system that experts call Markov state models. “Each computer is like a driver visiting different places and reporting back info on those locations so we can get a sense of the landscape.”

Individuals can participate by signing up and then installing software to their standard personal desktop or laptop. Participants can direct the software to run in the background and limit it to a certain percentage of processing power or have the software run only when the computer is idle.

When the software is at work, it’s conducting unique experiments designed and assigned by Bowman and his team back at Penn. Users can play scientist and watch the results of simulations and monitor the data in real time, or they can simply let their computer do the work while they go about their lives.

Read the full story at Penn Medicine News.

May 31, 2023May 30, 2023

Why is Machine Learning Trending in Medical Research but not in Our Doctor’s Offices?

by Melissa Pappas

Illustration of a robot in a white room with medical equipment. Machine learning (ML) programs computers to learn the way we do – through the continual assessment of data and identification of patterns based on past outcomes. ML can quickly pick out trends in big datasets, operate with little to no human interaction and improve its predictions over time. Due to these abilities, it is rapidly finding its way into medical research.

People with breast cancer may soon be diagnosed through ML faster than through a biopsy. Those suffering from depression might be able to predict mood changes through smart phone recordings of daily activities such as the time they wake up and amount of time they spend exercising. ML may also help paralyzed people regain autonomy using prosthetics controlled by patterns identified in brain scan data. ML research promises these and many other possibilities to help people lead healthier lives.

But while the number of ML studies grow, the actual use of it in doctors’ offices has not expanded much past simple functions such as converting voice to text for notetaking.

The limitations lie in medical research’s small sample sizes and unique datasets. This small data makes it hard for machines to identify meaningful patterns. The more data, the more accuracy in ML diagnoses and predictions. For many diagnostic uses, massive numbers of subjects in the thousands would be needed, but most studies use smaller numbers in the dozens of subjects.

But there are ways to find significant results from small datasets if you know how to manipulate the numbers. Running statistical tests over and over again with different subsets of your data can indicate significance in a dataset that in reality may be just random outliers.

This tactic, known as P-hacking or feature hacking in ML, leads to the creation of predictive models that are too limited to be useful in the real world. What looks good on paper doesn’t translate to a doctor’s ability to diagnose or treat us.

These statistical mistakes, oftentimes done unknowingly, can lead to dangerous conclusions.

To help scientists avoid these mistakes and push ML applications forward, Konrad Kording, Nathan Francis Mossell University Professor with appointments in the Departments of Bioengineering and Computer and Information Science in Penn Engineering and the Department of Neuroscience at Penn’s Perelman School of Medicine, is leading an aspect of a large, NIH-funded program known as CENTER – Creating an Educational Nexus for Training in Experimental Rigor. Kording will lead Penn’s cohort by creating the Community for Rigor which will provide open-access resources on conducting sound science. Members of this inclusive scientific community will be able to engage with ML simulations and discussion-based courses.

“The reason for the lack of ML in real-world scenarios is due to statistical misuse rather than the limitations of the tool itself,” says Kording. “If a study publishes a claim that seems too good to be true, it usually is, and many times we can track that back to their use of statistics.”

Such studies that make their way into peer-reviewed journals contribute to misinformation and mistrust in science and are more common than one might expect.

Read the full story in Penn Engineering Today.

May 30, 2023May 30, 2023

The Potential Futures of Neurotech

Brain technology offers all kinds of exciting possibilities — from treating conditions like epilepsy or depression, to simply maximizing brain health. But medical ethicists are concerned about potential dangers and privacy concerns. Roy Hamilton, Professor of Neurology in the Perelman School of Medicine, Director of the Penn Brain Science, Translation, Innovation, and Modulation (BrainSTIM) Center, and member of the Penn Bioengineering Graduate Group, spoke with WHYY about how brain stimulation is being used.

Listen to “Neurotech and the Growing Battle for Our Brains“

May 27, 2023May 26, 2023

Two from Penn Bioengineering Graduate Group Elected to the National Academy of Sciences

Four faculty from the University of Pennsylvania have been elected to the United States National Academy of Sciences (NAS). They are David Brainard of the School of Arts & Sciences; Duncan Watts of the Annenberg School of Communication, School of Engineering and Applied Science, and Wharton School; and Susan R. Weiss and Kenneth S. Zaret of the Perelman School of Medicine.

They join 120 members and 23 international members elected by their peers this year to NAS. Recognized for “distinguished and continuing achievements in original research,” this new class brings the total number of active members to 2,565 and of international members to 526.

Brainard and Zaret are members of the Penn Bioengineering Graduate Group.

David Brainard is the RRL Professor of Psychology, director of the Vision Research Center, and associate dean for the natural sciences in the School of Arts & Sciences. His research focuses on human vision, using both experiments and computer modeling of visual processing, to understand how the visual system deciphers information about objects from light entering the eye. Specifically, he and his lab are interested in color vision, conducting psychophysical experiments to investigate how the appearance of color is affected by an object’s surface properties and ambient light, and how color perception aids in identifying objects. Brainard is the recipient of many honors, including the Macbeth Award from the Inter-Society Color Council, Stein Innovation Award from Research to Prevent Blindness, and Edgard D. Tillyer Award from Optica. He is an elected member of the Society of Experimental Psychologists, a Silver Fellow of the Association for Research in Vision and Ophthalmology, and a Fellow of the Association for Psychological Science.

Kenneth S. Zaret is the Joseph Leidy Professor in the Department of Cell and Developmental Biology at the Perelman School of Medicine, director of the Institute for Regenerative Medicine, and a member of the Cell and Molecular Biology Graduate Program. His research focuses on gene regulation, cell differentiation, and chromatin structure, with a goal of elucidating these phenomena in the context of embryonic development and tissue regeneration. Pinpointing these aspects of development at the cellular level can serve as the basis for developing future therapeutics and experimental models that further scientists’ ability to understand and cure disease. Zaret has been the recipient of many honors, including a MERIT Award from the National Institutes of Health, the Stanley N. Cohen Biomedical Research Award, and election as a fellow of the American Association for the Advancement of Science.

Read the full announcement in Penn Today.

May 26, 2023

CiPD Fellows Recognized with Research Awards

Members of the inaugural cohort of fellows in the Center for Innovation and Precision Dentistry (CiPD)’s NIDCR T90/R90 Postdoctoral Training Program have been recognized for their research activities with fellows receiving awards from the American Association for Dental, Oral, and Craniofacial Research (AADOCR), the Society for Biomaterials, and the Osteology Foundation. All four of the honored postdocs are affiliated with Penn Bioengineering.

Zhi Ren won first place in the Fives-Taylor Award at the AADOCR Mini Symposium for Young Investigators. A postdoctoral fellow in the labs of Dr. Hyun (Michel) Koo at Penn Dental Medicine (and member of the Penn Bioengineering Graduate Group) and Dr. Kathleen Stebe of Penn Engineering, Dr. Ren’s research focuses on understanding how bacterial and fungal pathogens interact in the oral cavity to form a sticky plaque biofilm on teeth, which gives rise to severe childhood tooth decay that affects millions of children worldwide. In his award-winning study, titled “Interkingdom Assemblages in Saliva Display Group-Level Migratory Surface Mobility”, Dr. Ren discovered that bacteria and fungi naturally present in the saliva of toddlers with severe decay can form superorganisms able to move and rapidly spread on tooth surfaces.

Justin Burrell won second place in the AADOCR Hatton Competition postdoctoral category for his research. Dr. Burrell has been working with Dr. Anh Le in Penn Dental Medicine’s Department of Oral Surgery/Pharmacology and Dr. D. Kacy Cullen of Penn Medicine and Penn Bioengineering. Together, their interdisciplinary team of clinician-scientists, biologists, and neuroengineers have been developing novel therapies to expedite facial nerve regeneration and increase meaningful functional recovery.

Marshall Padilla earned third place at the Society for Biomaterials Postdoctoral Recognition Award Competition for a project titled, “Branched lipid architecture improves lipid-nanoparticle-based mRNA delivery to the liver via enhanced endosomal escape”. Padilla was also a finalist in the AADOCR Hatton Award Competition, presenting on a separate project titled, “Lipid Nanoparticle Optimization for mRNA-based Oral Cancer Therapy”. Both projects employ lipid nanoparticles, the same delivery vehicles used in the mRNA COVID-19 vaccine technology. A postdoctoral fellow in the lab of Dr. Michael J. Mitchell of Penn’s Department of Bioengineering, Dr. Padilla’s research focuses on developing new ways to enhance the efficacy and safety of lipid nanoparticle technology and its applications in dentistry and biomedicine. He has been working in collaboration with Dr. Shuying (Sheri) Yang and Dr. Anh Le in Penn Dental Medicine.

Dennis Sourvanos (GD’23, DScD’23) was the recipient of the Trainee Travel Grant award through the Osteology Foundation (Lucerne Switzerland). Dr. Sourvanos will be presenting his research related to medical dosimetry and tissue regeneration at the International Osteology Symposium in Barcelona, Spain (April 27^th – 29^th 2023). He also presented at the 2023 AADOCR/CADR Annual Meeting for his project titled, “Validating Head-and-Neck Human-Tissue Optical Properties for Photobiomodulation and Photodynamic Therapies.” Dr. Sourvanos has been working with Dr. Joseph Fiorellini in Penn Dental Medicine’s Department of Periodontics and Dr. Timothy Zhu in the Hospital of the University of Pennsylvania’s Department of Radiation Oncology and the Smilow Center for Translational Research (and member of the Penn Bioengineering Graduate Group).

Read the full announcement in Penn Dental Medicine News.

May 25, 2023

More 2023 SFB STAR Awards for Penn Bioengineering Students

Following up on our recent announcement of two Student Travel Achievement Recognition (STAR) Awards from the Society for Biomaterials (SFB) for members of the lab of Mike Mitchell, we are pleased to announce that two more Penn Bioengineering students also received STAR Awards!

Matthew Aronson and Alexandra Dumas are both members of the lab of Riccardo Gottardi, Assistant Professor in Pediatrics in the Perelman School of Medicine and in Bioengineering in the School of Engineering and Applied Science. Both presented their work at the recent 2023 SFB Annual Meeting and Exposition in San Diego, California in April 2023 and were honored with STAR Awards for their research.

The Gottardi Bioengineering and Biomaterials Laboratory studies treatment and function restoration for children with otolaryngologic disorders through the Children’s Hospital of Philadelphia (CHOP) in the Division of Otolaryngology.

Matthew Aronson is a third-year Ph.D. student in Bioengineering, an Ashton Fellow, and a NSF Fellow. His doctoral research focuses on studying pediatric airway diseases and disorders. More specifically, he is interested in how bacteria of the upper airway are responsible for the development and progression the disease subglottic stenosis, narrowing of the airway. In addition to understanding this devastating disease in the context of pediatric patients at CHOP, he also designed a novel drug-eluting endotracheal tube to deliver a selective antimicrobial peptide to function as a treatment modality for the prevention of the disease.

Alexandra Dumas is a rising fourth-year undergraduate in Bioengineering from Durban, South Africa. She is a PURM Fellow and a University Scholar. Her recent work in the Gottardi Lab focuses on using decellularized cartilage scaffolds to repair the meniscus and airway. After her undergraduate degree, she hopes to pursue a Ph.D. or M.D.-Ph.D. in bioengineering to pursue the design of new biomaterials for low-resource communities.

Read more stories featuring Gottardi and his team here.

May 19, 2023May 18, 2023

Michael Mitchell and Kyle Vining Win IDEA Prize from CiPD and Penn Health-Tech

Kyle Vining

Michael J. Mitchell, J. Peter and Geri Skirkanich Assistant Professor of Innovation in Bioengineering, and Kyle Vining, Assistant Professor in Materials Science and Engineering and in Penn Dental Medicine and member of the Penn Bioengineering Graduate Group, have been awarded the second-annual IDEA (Innovation in Dental Medicine and Engineering to Advance Oral Health) Prize, issued by the Center for Innovation & Precision Dentistry (CiPD) and Penn Health-Tech.

“Through their collaborative research, they are aiming to develop next-generation treatments for dental caries (tooth-decay) using lipid nanoparticles, the same delivery vehicles employed in the mRNA COVID-19 vaccine technology.

‘This project shows the type of innovative ideas and collaborations that we are kickstarting through the IDEA prize,’ says Dr. Michel Koo, co-director of the CiPD and Professor at Penn Dental Medicine. ‘This is a great example of synergistic interaction at the interface of engineering and oral health’ adds Dr. Kate Stebe, co-director of the CiPD and Professor at Penn Engineering.”

Read the full announcement in Penn Dental Medicine News.

May 17, 2023May 17, 2023

Franklin Medal Laureate Nader Engheta Honored at Sculpting Waves Symposium

by Devorah Fischler

(Left to Right) Vijay Kumar, Nemirovsky Family Dean of Penn Engineering, Nader Engheta, H. Nedwill Ramsey Professor in Electrical and Systems Engineering, and Michele Marcolongo, Drosdick Endowed Dean of Villanova University’s College of Engineering

On April 26, scholars from all over the world gathered at Villanova University to celebrate extraordinary innovation in the physics and technology of light.

The Franklin Institute Awards Laureate Symposium honored Nader Engheta, H. Nedwill Ramsey Professor in Electrical and Systems Engineering, Bioengineering, Materials Science and Engineering in the School of Engineering and Applied Science and in Physics and Astronomy in the College of Arts & Sciences at the University of Pennsylvania . The event heralded the awards gala held on April 27, where Engheta received the Benjamin Franklin Medal in Electrical Engineering from the Franklin Institute in Philadelphia, Pennsylvania.

The symposium, titled “Sculpting Waves with Complex Materials,” explored the richness and breadth of Engheta’s impact.

In a glass-paneled lecture hall nestled between flowering dogwoods and limber pines, speakers attested to Engheta’s technical acumen and intellectual creativity, describing his pathbreaking work in light-matter interaction.

Andrea Alù, Distinguished Professor at the City University of New York, Einstein Professor of Physics at the Graduate Center, CUNY and former Penn Engineering postdoctoral fellow, cited Engheta as “one of the original pioneers of the field of complex electromagnetic structures and modern metamaterials,” and the “father” of four influential fields: analog computing with metamaterials, plasmonic cloaking, non-zero-index metamaterials and optical nanocircuits.

Read the full story in Penn Engineering Today.

Watch the recording of the 2023 Franklin Institute Awards Ceremony on the Institute’s Youtube page.